Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1930 to 1979 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
242 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Rooted 0 23.9664 21.5733 1.11093
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Squared 21584.2 16770.2 1.28706
j domain containing protein 1. [swissprot;acc:q9ukb3] Ranked 1 227.357 254.15 1.11785
max protein. [swissprot;acc:p25912] Measured 4640.26 5704.87 1.22943
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Squared 42411.6 55802.1 1.31573
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Measured 0 729.216 642.343 1.13524
243 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Rooted 28.4971 25.6518 1.11092
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Measured 1 4246.95 5208.98 1.22652
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 0 1225.09 1079.36 1.13502
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Squared 8335.79 6506.81 1.28109
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Ranked 1251 1373 1.09752
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 1 227.357 254.15 1.11785
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Squared 42411.6 55802.1 1.31573
trophinin. [swissprot;acc:q12816] Rooted 137.446 120.823 1.13758
244 60s ribosomal protein l23a. [swissprot;acc:p29316] 0 22.6514 25.1571 1.11062
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Ranked 1 227.357 254.15 1.11785
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 14728.8 19330.8 1.31245
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Measured 0 1225.09 1079.36 1.13502
keratin associated protein 9.2. [refseq;acc:nm_031961] Ranked 10551.1 11579.9 1.09751
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Squared 80.1214 102.556 1.28001
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 1 146.94 167.046 1.13683
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Measured 4250.14 5211.25 1.22614
245 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Squared 8875.01 6768.05 1.31131
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted 0 22.6521 25.1534 1.11042
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Ranked 11867.6 13019 1.09702
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 1 4251.65 5212.33 1.22595
keratin associated protein 1.5. [refseq;acc:nm_031957] 0 1225.09 1079.36 1.13502
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted 1 146.94 167.046 1.13683
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Squared 0 10596.4 8278.87 1.27993
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 1 226.109 202.333 1.11751
246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared 8875.01 6768.05 1.31131
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 0 7273.2 9308.93 1.27989
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured 1 4252.66 5213.05 1.22583
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Ranked 0 10551.6 11573.7 1.09687
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Measured 1225.09 1079.36 1.13502
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Rooted 12.8935 14.3151 1.11026
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 1 146.94 167.046 1.13683
247 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Squared 0 20324.3 15893.2 1.2788
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 8875.01 6768.05 1.31131
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Measured 0 1225.09 1079.36 1.13502
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Ranked 10551.6 11573.7 1.09687
neurocalcin delta. [swissprot;acc:p29554] Rooted 12.8769 11.6055 1.10955
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 1 47.3621 53.8355 1.13668
rna-binding protein. [refseq;acc:nm_019027] Ranked 237.302 212.41 1.11719
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 6416.68 7865.15 1.22574
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 237.302 212.41 1.11719
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Rooted 0 30.7397 27.7265 1.10868
keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked 10551.6 11573.7 1.09687

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/